At tea, New Zealand were 43 without loss off 13 overs with Tom Latham on 27 and Martin Guptill not out 13 after Australia declared at 556 for four.
Guptill had a life on 12 when he was put down by Joe Burns fielding close to the bat off Mitchell Johnson.
Steve Smith declared Australia‘s innings on the dismissal of Khawaja an hour before tea.
Khawaja was out to a reverse sweep, spooning part-time spinner Kane Williamson to Guptill at backward point for 174.
Khawaja virtually gave away his wicket as word came out from the team dressing room of an impending declaration to end his 239-ball knock containing 18 fours and two sixes.
Adam Voges remained marooned on an effortless 83 off 127 balls, tantalisingly close to his first Test century.
It was a relief for the beleaguered Kiwis to get off the ground after 565 minutes and 130.2 overs, most of the second day without their injured pace spearheadTim Southee.
Southee pulled up with a back disc injury after delivering the last ball of his 24th over in the morning session. He left the field with the team trainer.
It remains to be seen whether Southee will bowl again in the Gabba Test if required.
New Zealand claimed the prized wicket of Australia skipper Smith early on the second morning.
The Black Caps bowled better lines and their field placements returned to traditional settings early on the second day after Thursday’s battering byAustralia.
They won an early reward with the scalp of the world’s second-ranked batsman Smith for 48.
Trent Boult, bowling much better than Thursday’s innocuous efforts, removed Smith with a beautiful in-swinger which clipped the off-bail.
Smith only added seven runs to his overnight score and the Black Caps celebrated a triumph of sorts after going to first day stumps at 389 for two.